No, I have exactly the same behavior in the master head and in 26.1
(from my distro).
Actually, after more tests I associate the issue with the global mode
only.
For example, this does not reproduce the issue, but the changes applies
to the "Customize Options" buffer itself only.
emacs -Q
M-x display-line-numbers-mode
M-x customize-variable RET display-line-numbers RET
But this:
emacs -Q
M-x global-display-line-numbers-mode
M-x customize-variable RET display-line-numbers RET
Does reproduce the bug and no changes applies at all.
I think it has to do with what Stefan suggested.